# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Sep 25 06:23:43 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2cnc3C(=O)NC=Nc23
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 CZU  CZU  "[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate"  ligand  46  31  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CZU
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 CZU  C2   C  CR16  0   0.165  56.3318  48.4638  -21.6456
 CZU  C4   C  CR56  0   0.490  54.4541  48.3230  -22.7772
 CZU  C5   C  CR56  0  -0.064  54.5915  46.9803  -23.0601
 CZU  C6   C  CR6   0   0.509  55.7426  46.2759  -22.5817
 CZU  O6   O  O     0  -0.454  56.0315  45.1034  -22.7295
 CZU  C1'  C  CH1   0   0.187  52.6899  50.0078  -23.2744
 CZU  C2'  C  CH1   0  -0.009  52.0224  50.5138  -24.5573
 CZU  C3'  C  CH1   0  -0.051  51.1327  51.6154  -23.9890
 CZU  C4'  C  CH1   0   0.011  50.7353  51.0310  -22.6139
 CZU  C5'  C  CH2   0  -0.222  49.3247  50.5071  -22.5109
 CZU  C8   C  CR15  0   0.103  52.7700  47.5758  -23.9505
 CZU  N1   N  NR16  0  -0.665  56.5680  47.1506  -21.8643
 CZU  N3   N  N     0  -0.447  55.2947  49.1067  -22.0737
 CZU  N7   N  N     0  -0.444  53.5285  46.5325  -23.7939
 CZU  N9   N  NR5   0  -0.546  53.2817  48.7022  -23.3615
 CZU  O1A  O  O     0  -0.667  49.6349  47.1380  -22.8324
 CZU  O1B  O  O     0  -0.643  50.2715  47.0408  -26.1897
 CZU  O1G  O  O     0  -0.669  46.6759  45.0128  -28.1292
 CZU  O2'  O  OH1   0  -0.644  52.9111  50.9852  -25.5179
 CZU  O2A  O  OH1   0  -0.711  47.2759  48.2098  -22.5441
 CZU  O2B  O  OH1   0  -0.726  48.4084  45.3697  -25.3912
 CZU  O2G  O  OH1   0  -0.729  45.6360  46.7346  -26.4413
 CZU  O3'  O  OH1   0  -0.660  51.9114  52.7756  -23.8600
 CZU  O3A  O  O2    0  -0.678  48.1377  47.7563  -24.8596
 CZU  O3B  O  O2    0  -0.676  47.9435  47.0960  -27.2174
 CZU  O3G  O  OH1   0  -0.711  46.0548  47.4656  -28.7787
 CZU  O4'  O  O2    0  -0.485  51.6585  49.9854  -22.3249
 CZU  O5'  O  O2    0  -0.572  49.0392  49.5979  -23.5833
 CZU  PA   P  P     0   1.475  48.6369  48.0875  -23.3468
 CZU  PB   P  P     0   1.511  48.8495  46.7922  -25.9281
 CZU  PG   P  P     0   1.454  46.5439  46.4115  -27.7000
 CZU  H1   H  HCR6  0   0.304  57.0854  48.9822  -21.0671
 CZU  H2   H  HCH1  0   0.258  53.4948  50.6916  -22.9820
 CZU  H3   H  HCH1  0   0.250  51.3662  49.7310  -24.9577
 CZU  H4   H  HCH1  0   0.258  50.2550  51.7938  -24.6209
 CZU  H5   H  HCH1  0   0.263  50.8202  51.8188  -21.8548
 CZU  H6   H  HCH2  0   0.270  48.6240  51.3383  -22.5969
 CZU  H7   H  HCH2  0   0.268  49.1712  50.0420  -21.5341
 CZU  H8   H  HCR5  0   0.305  51.8361  47.5804  -24.4892
 CZU  H10  H  HOH1  0   0.461  53.2527  50.2343  -26.0134
 CZU  H11  H  HOH1  0   0.509  47.0365  47.4278  -22.0256
 CZU  H12  H  HOH1  0   0.513  48.9117  44.6193  -25.7419
 CZU  H13  H  HOH1  0   0.509  44.8588  46.1656  -26.3466
 CZU  H14  H  HOH1  0   0.457  51.3510  53.4838  -23.5269
 CZU  H15  H  HOH1  0   0.508  46.3066  47.2581  -29.6901
 CZU  H16  H  HNR6  0   0.434  57.4177  46.7585  -21.4778

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 CZU  O1G  PG   double    1.469  0.020  1.469
 CZU  O3G  PG   single    1.586  0.020  1.586
 CZU  PG   O3B  single    1.631  0.020  1.631
 CZU  PG   O2G  single    1.585  0.020  1.585
 CZU  O3B  PB   single    1.605  0.020  1.605
 CZU  O1B  PB   double    1.467  0.020  1.467
 CZU  PB   O2B  single    1.583  0.020  1.583
 CZU  PB   O3A  single    1.606  0.020  1.606
 CZU  O2'  C2'  single    1.391  0.020  1.391
 CZU  O3A  PA   single    1.627  0.020  1.627
 CZU  O1A  PA   double    1.470  0.020  1.470
 CZU  O3'  C3'  single    1.403  0.020  1.403
 CZU  C3'  C2'  single    1.526  0.020  1.526
 CZU  C3'  C4'  single    1.546  0.020  1.546
 CZU  C2'  C1'  single    1.532  0.020  1.532
 CZU  PA   O5'  single    1.581  0.020  1.581
 CZU  PA   O2A  single    1.585  0.020  1.585
 CZU  O5'  C5'  single    1.435  0.020  1.435
 CZU  C1'  N9   single    1.436  0.020  1.436
 CZU  C1'  O4'  single    1.402  0.020  1.402
 CZU  C4'  C5'  single    1.508  0.020  1.508
 CZU  C4'  O4'  single    1.425  0.020  1.425
 CZU  N9   C8   aromatic  1.370  0.020  1.370
 CZU  N9   C4   aromatic  1.364  0.020  1.364
 CZU  C8   N7   aromatic  1.299  0.020  1.299
 CZU  C4   N3   single    1.347  0.020  1.347
 CZU  C4   C5   aromatic  1.379  0.020  1.379
 CZU  N3   C2   double    1.293  0.020  1.293
 CZU  N7   C5   aromatic  1.367  0.020  1.367
 CZU  C5   C6   single    1.432  0.020  1.432
 CZU  C2   N1   single    1.352  0.020  1.352
 CZU  C6   N1   single    1.400  0.020  1.400
 CZU  C6   O6   double    1.217  0.020  1.217
 CZU  C2   H1   single    0.930  0.020  1.080
 CZU  C1'  H2   single    0.970  0.020  1.090
 CZU  C2'  H3   single    0.970  0.020  1.090
 CZU  C3'  H4   single    0.970  0.020  1.090
 CZU  C4'  H5   single    0.970  0.020  1.090
 CZU  C5'  H6   single    0.970  0.020  1.090
 CZU  C5'  H7   single    0.970  0.020  1.090
 CZU  C8   H8   single    0.930  0.020  1.080
 CZU  O2'  H10  single    0.850  0.020  0.980
 CZU  O2A  H11  single    0.850  0.020  0.980
 CZU  O2B  H12  single    0.850  0.020  0.980
 CZU  O2G  H13  single    0.850  0.020  0.980
 CZU  O3'  H14  single    0.850  0.020  0.980
 CZU  O3G  H15  single    0.850  0.020  0.980
 CZU  N1   H16  single    0.860  0.020  1.020

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 CZU  H1   C2   N3   119.82  3.000
 CZU  H1   C2   N1   115.47  3.000
 CZU  N3   C2   N1   124.71  3.000
 CZU  N9   C4   N3   126.75  3.000
 CZU  N3   C4   C5   127.68  3.000
 CZU  N9   C4   C5   105.57  3.000
 CZU  N7   C5   C6   130.04  3.000
 CZU  C6   C5   C4   119.38  3.000
 CZU  N7   C5   C4   110.59  3.000
 CZU  N1   C6   O6   121.62  3.000
 CZU  O6   C6   C5   128.64  3.000
 CZU  N1   C6   C5   109.74  3.000
 CZU  H2   C1'  O4'  111.69  3.000
 CZU  H2   C1'  N9   106.31  3.000
 CZU  O4'  C1'  N9   109.25  3.000
 CZU  H2   C1'  C2'  109.72  3.000
 CZU  O4'  C1'  C2'  104.59  3.000
 CZU  N9   C1'  C2'  115.40  3.000
 CZU  H3   C2'  O2'  111.84  3.000
 CZU  H3   C2'  C3'  107.60  3.000
 CZU  O2'  C2'  C3'  112.65  3.000
 CZU  H3   C2'  C1'  109.30  3.000
 CZU  C3'  C2'  C1'  100.40  3.000
 CZU  O2'  C2'  C1'  114.33  3.000
 CZU  H4   C3'  O3'  111.27  3.000
 CZU  H4   C3'  C4'  111.62  3.000
 CZU  O3'  C3'  C4'  111.93  3.000
 CZU  H4   C3'  C2'  111.69  3.000
 CZU  C4'  C3'  C2'  102.02  3.000
 CZU  O3'  C3'  C2'  107.92  3.000
 CZU  H5   C4'  O4'  109.66  3.000
 CZU  H5   C4'  C5'  105.94  3.000
 CZU  O4'  C4'  C5'  109.71  3.000
 CZU  H5   C4'  C3'  108.91  3.000
 CZU  O4'  C4'  C3'  106.93  3.000
 CZU  C5'  C4'  C3'  115.62  3.000
 CZU  H7   C5'  H6   107.74  3.000
 CZU  H7   C5'  O5'  111.75  3.000
 CZU  H6   C5'  O5'  107.23  3.000
 CZU  H7   C5'  C4'  109.89  3.000
 CZU  H6   C5'  C4'  109.31  3.000
 CZU  O5'  C5'  C4'  110.81  3.000
 CZU  H8   C8   N9   122.32  3.000
 CZU  H8   C8   N7   124.71  3.000
 CZU  N9   C8   N7   112.97  3.000
 CZU  H16  N1   C6   116.63  3.000
 CZU  H16  N1   C2   117.45  3.000
 CZU  C6   N1   C2   125.91  3.000
 CZU  C4   N3   C2   112.58  3.000
 CZU  C8   N7   C5   104.81  3.000
 CZU  C8   N9   C1'  128.28  3.000
 CZU  C8   N9   C4   106.06  3.000
 CZU  C1'  N9   C4   125.53  3.000
 CZU  H10  O2'  C2'  108.53  3.000
 CZU  H11  O2A  PA   114.91  3.000
 CZU  H12  O2B  PB   115.36  3.000
 CZU  H13  O2G  PG   114.69  3.000
 CZU  H14  O3'  C3'  108.49  3.000
 CZU  PB   O3A  PA   127.23  3.000
 CZU  PG   O3B  PB   129.99  3.000
 CZU  H15  O3G  PG   114.70  3.000
 CZU  C4'  O4'  C1'  109.12  3.000
 CZU  PA   O5'  C5'  122.98  3.000
 CZU  O5'  PA   O3A   97.67  3.000
 CZU  O5'  PA   O2A  102.74  3.000
 CZU  O3A  PA   O2A  102.89  3.000
 CZU  O2A  PA   O1A  117.10  3.000
 CZU  O5'  PA   O1A  119.77  3.000
 CZU  O3A  PA   O1A  113.70  3.000
 CZU  O3B  PB   O3A   99.83  3.000
 CZU  O3A  PB   O2B  100.97  3.000
 CZU  O3B  PB   O2B  106.57  3.000
 CZU  O3A  PB   O1B  116.53  3.000
 CZU  O2B  PB   O1B  118.87  3.000
 CZU  O3B  PB   O1B  111.83  3.000
 CZU  O3G  PG   O3B  100.78  3.000
 CZU  O3B  PG   O2G   99.85  3.000
 CZU  O3G  PG   O2G  103.18  3.000
 CZU  O2G  PG   O1G  118.52  3.000
 CZU  O3B  PG   O1G  114.14  3.000
 CZU  O3G  PG   O1G  117.51  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 CZU  CONST_01  N7   C8   N9   C4      0.00   0.0  0
 CZU  CONST_02  C8   N7   C5   C4      0.00   0.0  0
 CZU  CONST_03  C8   N9   C4   C5      0.00   0.0  0
 CZU  CONST_04  N9   C8   N7   C5      0.00   0.0  0
 CZU  CONST_05  N9   C4   C5   N7      0.00   0.0  0
 CZU  CONST_06  C1'  N9   C4   C5    180.00   0.0  0
 CZU  CONST_07  N7   C8   N9   C1'   180.00   0.0  0
 CZU  CONST_08  N3   C4   N9   C1'     0.00   0.0  0
 CZU  CONST_09  C5   C6   N1   C2      0.00   0.0  0
 CZU  CONST_10  N1   C2   N3   C4      0.00   0.0  0
 CZU  CONST_11  N3   C2   N1   C6      0.00   0.0  0
 CZU  CONST_12  O6   C6   N1   C2    180.00   0.0  0
 CZU  CONST_13  H8   C8   N9   C4    180.00   0.0  0
 CZU  CONST_14  H8   C8   N7   C5    180.00   0.0  0
 CZU  CONST_15  H8   C8   N9   C1'     0.00   0.0  0
 CZU  CONST_16  H1   C2   N3   C4    180.00   0.0  0
 CZU  CONST_17  H16  N1   C6   C5    180.00   0.0  0
 CZU  CONST_18  H1   C2   N1   C6    180.00   0.0  0
 CZU  CONST_19  H16  N1   C2   N3    180.00   0.0  0
 CZU  CONST_20  H16  N1   C6   O6      0.00   0.0  0
 CZU  CONST_21  H16  N1   C2   H1      0.00   0.0  0
 CZU  Var_01    PA   O5'  C5'  C4'   119.55  30.0  2
 CZU  Var_02    O3A  PA   O5'  C5'   167.74  30.0  1
 CZU  Var_03    O1A  PA   O5'  C5'   -69.28  30.0  1
 CZU  Var_04    O2A  PA   O5'  C5'    62.59  30.0  1
 CZU  Var_05    PB   O3A  PA   O1A   -16.50  30.0  2
 CZU  Var_06    PG   O3B  PB   O1B   149.23  30.0  1
 CZU  Var_07    PA   O3A  PB   O1B   -52.24  30.0  3
 CZU  Var_08    PB   O3B  PG   O1G   -68.25  30.0  3
 CZU  Var_09    PB   O3A  PA   O2A  -144.15  30.0  2
 CZU  Var_10    PG   O3B  PB   O2B    17.79  30.0  1
 CZU  Var_11    PA   O3A  PB   O2B    78.03  30.0  3
 CZU  Var_12    PB   O3B  PG   O2G    59.26  30.0  3
 CZU  Var_13    PG   O3B  PB   O3A   -86.87  30.0  1
 CZU  Var_14    PA   O3A  PB   O3B  -172.79  30.0  3
 CZU  Var_15    PB   O3B  PG   O3G   164.84  30.0  3
 CZU  Var_16    PB   O3A  PA   O5'   110.83  30.0  2
 CZU  Var_17    H6   C5'  O5'  PA   -121.22  30.0  3
 CZU  Var_18    H7   C5'  O5'  PA     -3.37  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 CZU  chir_01  C1'  C2'  N9   O4'  positiv
 CZU  chir_02  C2'  O2'  C3'  C1'  positiv
 CZU  chir_03  C3'  O3'  C4'  C2'  positiv
 CZU  chir_04  C4'  O4'  C3'  C5'  negativ
 CZU  chir_05  PA   O1A  O5'  O2A  both
 CZU  chir_06  PB   O2B  O1B  O3B  both

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 CZU  plan-1  C2   0.020
 CZU  plan-1  C4   0.020
 CZU  plan-1  C5   0.020
 CZU  plan-1  C6   0.020
 CZU  plan-1  O6   0.020
 CZU  plan-1  C1'  0.020
 CZU  plan-1  C8   0.020
 CZU  plan-1  N1   0.020
 CZU  plan-1  N3   0.020
 CZU  plan-1  N7   0.020
 CZU  plan-1  N9   0.020
 CZU  plan-1  H1   0.020
 CZU  plan-1  H8   0.020
 CZU  plan-1  H16  0.020

